This week the government announced £1bn investment in scientific research - mainly into biotechnologies, with their potential for advances in medicine and general human welfare. Reflective taxpayers could think of few better uses for their money than investment in the future of us all, so the initiative is welcome.

Last week the government announced increased funding for religion-based schools. The contradiction with the foregoing is dramatic. Adherence to ancient traditions of religious belief is divided among many differing and often competing minorities in our society. Giving them taxpayers' money to run schools in which new generations are indoctrinated in these varying and exclusive ancient belief systems is fundamentally wrong on many counts, chief among them the following three.

First, by using our tax money to subsidise religion-based schools, the government forces those many of us who are opposed to superstitious beliefs and practices to contribute against our wills to their perpetuation. Religion is a matter of private conscience and choice, and as such is not a proper target for public support. If minorities wish to have their children taught in schools which premise belief in gods, astrology, space aliens or elves, they should pay for it themselves.

Second, religion is harmful both to individuals and society when it becomes publicly institutionalised. It harms individuals by distorting human nature through repressive moralities and the inculcation of false beliefs, fears and hopes. It harms society by causing conflicts, wars and persecutions, as everywhere evidenced by religious history including the present. It ought therefore to remain in the private sphere along with other personal matters, like sexual preference (perhaps it needs its own Section 28).

It is unacceptable to people who, for these reasons, are opposed to religion, to see young children being indoctrinated into it. Children should emphatically not be taught as "facts" the myths and legends of ancient religious traditions: to do this to anyone unable to evaluate their credibility is a form of brainwashing or even indeed abuse. Public funds should never be used to that end.

Third, by giving money to a variety of religious organisations - Christian, Muslim, Jewish, Sikh, Hindu - historically and theologically at odds (which indeed mutually blaspheme one another's faiths), the government is helping to entrench divisions. Children of all backgrounds ought to be educated together for greater mutual understanding, not educated apart in religious ghettos, thereby perpetuating the exclusivity and mistrust which must arise if people believe their religion is the only true one and everyone else is wrong - perhaps even that they are dangerous fanatics.

The variety of religious traditions should of course be taught in schools - but as historical phenomena alongside astrology, magic, and other fads of mankind's earlier ignorance. This would not please the religions, who are avid to indoctrinate young people since that is one of their chief means of survival. Few who first meet religion in adulthood are able to take it seriously; priests know that to keep the old faiths alive, they have to get their hands on children. Some religion-based schools are good because they are highly selective - not just (despite disclaimers) in obvious but in covert ways.

Keen, supportive, educated middle-class parents are a strongly self-selecting group. Small class sizes play a crucial part. The government ought to put real resources into making all state schools as good as the best church schools, and not supporting the latter as a cheap alternative to private education for middle-class parents who cannot or will not afford it.

No doubt the government believes it is encouraging good education while showing a kindly face to the different traditions in our society. But the reality is otherwise. It is troubling to find the government funding past superstitions and future science simultaneously, as if unaware of the dramatic inconsistency, and unconcerned about the fact that it is using public money - including the taxes of the many who are emphatically unwilling - to do the former. There is a human rights implication here, which someone would do well to explore in our courts.